Searching journal content for articles similar to LeBaron von Baeyer et al. 34 (1): 1.

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  1. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...models (HMMs) (Tang et al. 2006; Corbett-Detig and Nielsen 2017; Browning et al. 2018, 2023) become computationally expensive and slow when faced with biobank-sized data, neural networks can provide a powerful alternative.Genomic sequence compressionThe storage and transmission of high...
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  2. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ..., it often 24 struggles with interpretability because of its black-box nature. We evaluate 12 ML models 25 alongside GBLUP and BayesR to identify key factors influencing genomic prediction 26 performance across traits with different genetic architectures in multiple agricultural species, 27 including pigs...
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  3. Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...(Figures 4 (E) and (F)). As to the reason why spRefine did not work well290 in multiple cell-state differentiation, we speculated that the smoothing and denoising291 effects of imputation on gene expression may have masked some very strong signals292 that are supposed to be associated...
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  4. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...Caenorhabditis briggsae and its sister species Caenorhabditis nigoni provide an ideal model system to address this question, as they exhibit extensive genomic divergence with limited gene flow from C. briggsae to C. nigoni. Despite previous comparative genomic studies, a comprehensive analysis of both...
  5. Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
    • Gilad Barshad and
    • Charles G. Danko
    Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
    ...to the end of the TAD, the process of loop extrusion could nevertheless constrain the three-dimensional diffusion to a smaller space, by preventing diffusion further apart than the current constraints placed by the loop. Indeed, these mechanisms may explain why cohesin depletion has a larger impact...
  6. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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  7. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...Medhat Mahmoud1,4, Daniel P. Agustinho1,4 and Fritz J. Sedlazeck1,2,3 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3Department of Computer Science, Rice...
  8. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
  9. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...and Roeder 1999; Yang et al. 2011). In the GWAS of common variants for the smooth phenotype, the genomic inflation factor (denoted by λgc) was 1.101 (confidence intervals [CI]: 1.084–1.118) when including SPCs in the model compared with 5.410 (CI: 5.305–5.517) when including PCs in the model, indicating...
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  10. Research: The genomic consequences and persistence of sociality in spiders
    • Jilong Ma,
    • Jesper Bechsgaard,
    • Anne Aagaard,
    • Palle Villesen,
    • Trine Bilde,
    • and Mikkel Heide Schierup
    Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
    ...to an increasingly female-biased sex ratio. This almost deterministic genomic response to sociality may explain why social spider lineages do not persist. What causes species extinction is not clear, but either could be selfish meiotic drive eliminating the production of males or could be an inability to retain...
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